Mine sits on the saddle with a lock cable so it can't fall far enough to hit anything. The cable goes through the rear rack and up to the tank bag. Last time I left one on the ground some asshat helped himself/herself to it (it was hidden behind the front wheel in my work's parking ramp - because I forgot to move the cable between bikes :eek1). Took me over a year to find another in that pattern.

Another advantage of locking it to the seat is that no one can test sit on MY bikes uninvited

I usually carry it with me, but if its going to be a long stop I have a bag that has a steel mesh between two layers that you can lock to the bike. Keeps out the rain and other unwanted things. I have known people who have cable locked their helmet to the bike come back and find its been pissed in!